Major microspecies

I need the major microspecies (ionized form) at a given pH.


I see that cxcalc can output this in form of a SMILES table, for example at pH=0:

Code:

$ cxcalc majorms -H 0 "CNCC([O-])=O" id      major-ms 1       C[NH2+]CC(O)=O

Is it possible to write the ionized form in SDF format?

Yes, you can specify the output format in the -f option of the majorms plugin in cxcalc but you also need to prevent the molecule ID and table header printout by the cxcalc option -N ih to get a valid SDF:

Code:

cxcalc -N ih -o majorms.sdf majorms -H 0 -f sdf test.sdf